GBE · GBE The Author(s) 2015. Published by Oxford University Press on behalf of the Society for...

Comparative Genomics of Sibling Fungal Pathogenic Taxa

Identifies Adaptive Evolution without Divergence in

Pathogenicity Genes or Genomic Structure

Fabiano Sillo1,y, Matteo Garbelotto2,y, Maria Friedman2, and Paolo Gonthier1,*1Department of Agricultural, Forest and Food Sciences, University of Torino, Grugliasco, Italy2Department of Environmental Science, Policy and Management, University of California, Berkeley

*Corresponding author: E-mail: [email protected] authors contributed equally to this work.

Associate editor: Takashi Gojobori

Accepted: October 26, 2015

Data deposition: Sequences of raw reads, alignments (BAM files), and de novo assembled genomes have been deposited at the EMBL database

ENA—European Nucleotide Archive as a project under the accession PRJEB8921.

Abstract

It has been estimated that the sister plant pathogenic fungal species Heterobasidion irregulare and Heterobasidion annosum may

have been allopatrically isolated for 34–41 Myr. They are now sympatric due to the introduction of the first species from North

America into Italy, where they freely hybridize. We used a comparative genomic approach to 1) confirm that the two species are

distinct at the genomic level; 2) determine which gene groups have diverged the most and the least between species; 3) show that

their overall genomic structures are similar, as predicted by the viability of hybrids, and identify genomic regions that instead are

incongruent;and 4) test thepreviously formulatedhypothesis thatgenes involved inpathogenicitymaybe lessdivergentbetweenthe

two species than genes involved in saprobic decay and sporulation. Results based on the sequencing of three genomes per species

identified a high level of interspecific similarity, but clearly confirmed the status of the two as distinct taxa. Genes involved in

pathogenicity were more conserved between species than genes involved in saprobic growth and sporulation, corroborating at

the genomic level that invasiveness may be determined by the two latter traits, as documented by field and inoculation studies.

Additionally, the majority of genes under positive selection and the majority of genes bearing interspecific structural variations were

involved either in transcriptional or in mitochondrial functions. This study provides genomic-level evidence that invasiveness of

pathogenic microbes can be attained without the high levels of pathogenicity presumed to exist for pathogens challenging naıve

hosts.

Key words: plant pathogenic fungi, Heterobasidion, structural variations, dN/dS, allopatric speciation.

Introduction

Theories predict that drift and differential selection will in-

crease interspecific genetic variation in species diverging allo-

patrically (Turelli et al. 2001). However, in the absence of

strong differential selective pressure, ancestral polymorphisms

may be retained. For instance, ancestral polymorphisms may

be retained due to the necessity of maintaining a vital biolog-

ical function or due to the presence of strong disruptive selec-

tion pressures. A classical example is that of interfertility: it has

been shown that although sympatric and genetically diverging

protospecies may experience a reinforcement of genetic

isolation through newly developed intersterility, there is little

selection pressure to develop intersterility when two divergent

populations become geographically isolated (Kohn 2005). In

the Kingdom Fungi, it has been reported that differences in

genomic architecture mirror the interplay of different muta-

tional processes with constraints provided by their character-

istic population biology (Stukenbrock and Croll 2014).

Different types of genomic rearrangements leading to

changes in genomic architecture and gene expression, as

well as amino acid substitutions and duplication events, may

play a crucial role in promoting adaptive divergence across

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species. A genomic analysis of two allopatrically diverged sister

taxa may thus reveal substantial structural genomic variations

in all regions subject to differential selective pressure. In the

case of plant pathogens, it has been commonly assumed that

differential adaptive selection on allopatric species leads to

divergent evolution of genes involved in plant–pathogen in-

teractions, resulting in greater virulence of pathogens against

noncoevolved plant hosts (Parker and Gilbert 2004). Although

this appears to be the case for several pathogens, to our

knowledge no research has fully addressed adaptive divergent

evolution in plant pathogens involving traits related to general

fitness and in particular to transmission. The narrow focus on

pathogenicity has stifled a broader understanding of divergent

evolutionary mechanisms for pathogens (Gonthier and

Garbelotto 2013).

The Heterobasidion annosum species complex includes five

species of plant pathogens hypothesized to have progressively

diverged either in sympatry or in allopatry, depending on the

species pair, starting 60 Ma and ending approximately 14 Ma

(Dalman et al. 2010). Heterobasidion species can be both

saprotrophic decomposers and necrotrophic pathogens.

Although this is not uncommon for wood inhabiting microor-

ganisms (Aguilar-Trigueros et al. 2014), Heterobasidion spp.

differ from other fungi because the saprotrophic phase can

occur both before and after the necrotrophic one. It is the

saprotrophic phase preceding the necrotrophic one that is

quite unique (Olson et al. 2012; Garbelotto and Gonthier

2013). In fact, it has been repeatedly demonstrated that for

Heterobasidion species primarily associated with the genus

Pinus, the majority of primary infection occurs as fungal ge-

notypes saprobically colonize pine stumps. Colonized stumps

subsequently become the major source of infection for adja-

cent trees through direct contagion along interconnected root

systems.

In nature, only two pairs of species have been documented

to hybridize: the sympatric Heterobasidion irregulare and

Heterobasidion occidentale in western North America

(Garbelotto et al. 1996; Lockman et al. 2014), and the allo-

patrically diverged H. irregulare and H. annosum in Italy

(Gonthier et al. 2007; Gonthier and Garbelotto 2011).

Divergent speciation between H. irregulare and H. occidentale

has been estimated to have occurred 30–40 Ma, and the two

species are known to have substantially different host prefer-

ence (Dalman et al. 2010; Otrosina and Garbelotto 2010;

Garbelotto and Gonthier 2013) and limited interspecific inter-

fertility (Harrington et al. 1989). Thus, it is not surprising that

the frequency of hybridization in nature appears to be ex-

tremely low and that genomic abnormalities have been re-

ported to be associated with these hybrids (Garbelotto et al.

2004). Conversely, H. irregulare and H. annosum have

become sympatric only recently when H. irregulare was trans-

ported from North America to Italy, presumably in 1944

(Gonthier et al. 2004). In spite of a history of allopatry lasting

34–41 Ma, the two species have maintained a comparable

host preference for the genus Pinus and are known to be

highly interfertile (Garbelotto and Gonthier 2013). Massive

hybridization has resulted in the generation of hybrid

swarms (Gonthier and Garbelotto 2011), a phenomenon

known to occur for plants and animals, but so far unreported

for the fungi (Brasier 2000). Studies on the fitness of hybrids

have highlighted a significant role apparently played by the

mitochondrial genome (Olson and Stenlid 2001; Garbelotto

et al. 2007), but the mechanisms of this role still remain elu-

sive. Nonetheless, fitness regulated by mitochondrial factors

has been reported for a variety of organisms (Jiang et al. 2008;

Shen et al. 2010; Greiner and Bock 2013).

The movement of H. irregulare from North America into

Italy has resulted not only in the creation of hybrid H. irregulare

� H. annosum swarms but also in an ongoing invasion process

by the exotic species which is seemingly outcompeting the

native one (Gonthier et al. 2007, 2012). Surprisingly, recipro-

cal inoculation studies and field monitoring efforts have dem-

onstrated that the two species have comparable pathogenicity

on Eurasian and North American pine species, but differ sig-

nificantly in saprobic and sporulation potential (Garbelotto

et al. 2010; Giordano et al. 2014; Gonthier et al. 2014).

Despite advances in the understanding of genomic evolu-

tion due to hybridization events among species that have long

diverged (Clarke et al. 2002; Rieseberg et al. 2003), only scant

information is available on the evolution of genomes of fungal

pathogens undergoing hybridization (Brasier and Kirk 2010).

A comparative genomic analysis would help 1) elucidating the

genomic structure of sibling taxa that despite undergoing spe-

ciation in allopatry, have maintained a similar biology and host

preference; 2) determining the mechanisms underlying the

current massive hybridization between the two sibling species,

H. irregulare and H. annosum; and 3) the identification of

genomic regions providing the advantage the invasive species

H. irregulare has over the native H. annosum. Understanding

which genomic traits may confer an advantage to an invasive

species may be pivotal to identify factors explaining the inva-

siveness of plant pathogens (Gonthier and Garbelotto 2013).

Such understanding might also help to discover genes that

may lead to significant adaptive changes if introgressed be-

tween species.

In this study, we report on the genome sequencing of three

H. irregulare and three H. annosum genotypes, their reciprocal

relationship, and their comparison to the reference genome of

H. irregulare isolate TC 32-1 sequenced in 2012 (Olson et al.

2012). By using a comparative genomics approach, our spe-

cific goals were 1) to confirm that H. irregulare and H. anno-

sum are clearly distinct species in spite of their high

morphological and ecological similarities (Otrosina and

Garbelotto 2010); 2) to show that in spite of high genetic

divergence, the structure of the two genomes has remained

extremely similar, as predicted by the ease at which the two

species generate fertile hybrids (Gonthier and Garbelotto

2011); 3) to identify the main sources of variation in the

Comparative Genomics of Heterobasidion species GBE

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genomes of the two sibling species; 4) to identify highly con-

served gene families and genomic regions involved in the suc-

cessful adaptation of both species in similar forest habitats

located in two different continents; and 5) to test whether

genes involved in saprobic wood decay and fruiting/sporula-

tion may be significantly different between the two species, as

expected based on published experimental evidence

(Garbelotto et al. 2010; Giordano et al. 2014), thus providing

a possible explanation on which traits may confer H. irregulare

with an establishment advantage over H. annosum.

Materials and Methods

Biological Materials and DNA Extraction

A total of six haploid genotypes, three of H. irregulare and

three of H. annosum, from four Italian sites were used in this

study (table 1). Genotypes were deposited at the Mycotheca

Universitatis Taurinensis (MUT) (table 1). Based on a previous

analysis (Gonthier and Garbelotto 2011), none of the geno-

types showed significant genetic admixing. All genotypes de-

rived from single spores collected on woody spore traps and

were grown in 2% malt extract liquid medium at 25 �C for 10

days before being harvested. Fungal tissues (200 mg) were

collected using a vacuum pump, freeze dried over night,

and ground using glass beads (diameter 0.2 and 0.4 mm) in

a FastPrepTM Cell Disrupter (FP220-Qbiogene). Total DNA ex-

traction was performed using DNeasy Plant Mini Kit (Qiagen

Inc., Valencia, CA), following manufacturer instructions. DNA

quantification was carried out by using the ND-1000 spectro-

photometer (NanoDrop Technologies, Wilmington, DE). DNA

quality was assessed both by electophoresis of extracted DNA

on a 1% agarose gel and by using a chip-based microcapillary

electrophoresis system (Experion, Bio-Rad Laboratories, Hemel

Hempstead, UK).

Genome Sequencing, Mapping, and De Novo Assembly

Paired-end (PE) 100-bp DNA libraries were prepared for each

genotype and sequenced using an Illumina HiSeq 2000 plat-

form at the Functional Genomics Laboratory of the University

of California, Berkeley. The software FASTQC (http://www.

bioinformatics.bbsrc.ac.uk/projects/fastqc/, Last accessed

November 16, 2015) was used to check read quality. Low-

quality 100-bp reads (Q score < 22) were discarded. Raw

reads of each genotype were aligned to the reference H.

irregulare TC 32-1 genome (Olson et al. 2012) available in

the JGI database (Heterobasidion annosum v2.0: Project:

16080, Heterobasidion_annosum.allmasked.fasta) using the

Burrows-Wheeler Aligner MEM (BWA-MEM) optimized for

100-bp PE reads (Li and Durbin 2009). The output was used

to generate mapping files in SAM format, which were then

converted in BAM format, ordered, and indexed. Unmapped

reads of H. annosum genotypes were assembled in contigs

with Velvet 1.2.08 (Zerbino and Birney 2008) by setting k-mer

= 39. Open-reading frame prediction on contigs produced by

assembly of unmapped reads was performed by using

Augustus v2.5.5 (Stanke and Morgenstern 2005) with a train-

ing set from Coprinus species and the following parameters:

gene model = partial; protein, introns, start, stop, cds, coding

seq, gff3, and UTR = on. The predicted amino acid sequences

were identified by similarity search in the NCBI (National

Center for Biotechnology Information) nonredundant protein

sequence (NR) database (http://www.ncbi.nlm.nih.gov, Last

accessed November 16, 2015) and were subsequently char-

acterized by using BLAST2GO (Conesa et al. 2005).

De novo assembly of reads was performed using Velvet

1.2.08 (Zerbino and Birney 2008) with k-mer = 39 bp,

chosen after optimization tests using k-mer sizes 37, 39,

41, and 43. Draft assemblies were refined and gaps were

minimized using IMAGE2 (Swain et al. 2012) set at ten iter-

ations and taking as inputs both unassembled reads and

contigs in FASTA format generated by the Velvet assembly

process. The final ordering of contigs and scaffolding process

were performed with CONTIGuator (Galardini et al. 2011),

by using the genome of H. irregulare TC 32-1 as a backbone

(Heterobasidion annosum v2.0: Project: 16080,

Heterobasidion_annosum.AssembledScaffolds.fasta). De

novo assembly drafts were compared by using

progressiveMauve (Darling et al. 2010). Sequences of raw

reads, alignments (BAM files), and de novo assembled

genomes were submitted to the EMBL database ENA—

European Nucleotide Archive as a project under the

accession number PRJEB8921.

The alignment of reads to the reference genome was

used to identify putative H. annosum structural variations

(SVs), copy number variations (CNVs), and single

nucleotide polymorphisms (SNPs)/InDels (insertions/deletions).

Table 1

Summary of Heterobasidion Genotypes Sequenced

ID Code Species Geographic Origin MUT Accession No.

9OA Heterobasidion irregulare Castelfusano Pinewood Urban Park; Rome (RM) MUT00003629

48NB Heterobasidion irregulare Castelfusano Pinewood Urban Park; Rome (RM) MUT00003627

49SA Heterobasidion irregulare Castelfusano Pinewood Urban Park; Rome (RM) MUT00003628

137OC Heterobasidion annosum Circeo National Park/the forest of Sabaudia; Sabaudia (LT) MUT00003656

BM42NG Heterobasidion annosum Mesola Forest; Mesola (FE) MUT00003543

109SA Heterobasidion annosum Feniglia Pinewood; Grosseto (GR) MUT00003538

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Phylogenomic analysis was also performed on the alignment

of reads to the reference genome carried out with bowtie2

(Langmead et al. 2009), which is integrated in the phyloge-

netic software REALPHY (Bertels et al. 2014). De novo assem-

bly drafts were compared to confirm SVs detected and were

used to perform the simple sequence repeat (SSR) survey.

Details on the abovementioned analysis are provided in the

next paragraphs.

Identification of Putative SVs

SVs among genomes (i.e., large insertions, large deletions,

inversions, intratranslocations, and intertranslocations) were

predicted by using SVDetect v. r0.7 m (Zeitouni et al. 2010)

on filtered SAM files produced by the alignment of reads to

the reference genome containing both unmapped and abnor-

mally mapped reads for each genotype. The SAMtools pack-

age (Li et al. 2009) was used to filter SAM files. Average insert

sizes (m) and standard deviations (s) were calculated for each

genotype and were used to determine the minimum threshold

required for the detection of putative insertions and deletions.

Identified SVs were filtered by quality based on the number of

reads supporting the predicted variation, that is, SVs sup-

ported by less than 20 reads were discarded. SVs shared

among H. annosum genotypes but absent among H. irregu-

lare genotypes were putatively considered to be species-spe-

cific. Putative SVs, that is, inversions and translocations, were

confirmed through comparative genomic analyses among de

novo assembly drafts performed by using progressiveMauve

(Darling et al. 2010). SVs were then manually scored and

compared with those identified by SVDetect. Putative SVs in

each scaffold and read depth for two representative geno-

types were visualized as circular plots drawn with the Circos

software v. 0.64 (Krzywinski et al. 2009). A chi-square test

was used to determine whether SVs occurred more frequently

in some scaffolds. This test was performed using absolute

frequencies of SVs per scaffold and assuming an equal prob-

ability of occurrence for each scaffold.

Genes in regions containing inversions and translocations

were detected using the BEDtools package “intersect”

(Quinlan and Hall 2010). Transcripts were identified by ID

and their corresponding encoded proteins were analyzed

with BLAST2GO (Conesa et al. 2005) to search for homologs

and to determine their Gene Ontology (GO). Significant dif-

ferences in frequencies of GO terms compared with all H.

irregulare gene models were assessed by using a Fisher’s

exact test (Bluthgen et al. 2005) with the false discovery rate

(FDR) control, which takes into account multiple comparisons

(Al-Shahrour et al. 2004).

Identification of Putative CNVs

The CNV analysis was performed with CNV-seq (Xie and

Tammi 2009) on alignment files after read-count normaliza-

tion using a 10�6 P-value threshold. The purpose of this

analysis was to identify differences in sequence coverage,

that is, to identify variations in copy numbers of mapped se-

quences using a 2-kb sliding window between the consensus

reads data sets of the two species. Results were plotted and

drawn using the cnv package and a procedure in R language

customized in house. As for inverted and translocated geno-

mic regions, a BLAST2GO analysis was performed on genes

detected in regions affected by significant CNV events (P

value<0.05, log2 > 5). Significant differences in frequencies

of GO terms compared with all H. irregulare gene models

were assessed by using a Fisher’s exact test (Bluthgen et al.

2005) with FDR control.

Identification of Putative SNPs/InDels

A pileup procedure on SAMtools v. 0.1.18 (Li et al. 2009)

followed by quality filtering on VCFtools v 0.1.12 a (Danecek

et al. 2011) was used to identify SNPs/InDels, with “–minQ”

set to 20 and “–min-meanDP” set to 5. By using the tool vcf-

isec, the SNPs/InDels consensus data set for H. annosum ge-

notypes was compared with that for H. irregulare genotypes

to identify sequence variants present exclusively in H. anno-

sum. The resulting SNPs/InDels panel was annotated with the

snpEff package (Cingolani et al. 2012) using the gene model

catalog database available for the reference genome

(Hannosum_v2.FilteredModels1.gff.gz). The snpEff package

was used to determine the genomic position of SNPs/InDels

(intergenic/exon/intron) and to identify synonymous and

nonsynonymous changes. To confirm putative H. annosum

SNPs/InDels, four loci involved in sabrobic growth, four in-

volved in sporulation, and two related to pathogenicity

(Olson et al. 2012) were randomly selected to be amplified,

sequenced and compared on five additional H. irregulare ge-

notypes and five H. annosum genotypes (listed in supplemen-

tary table S1, Supplementary Material online). Primers

targeting the selected loci were designed by using

Primer3Plus (http://www.bioinformatics.nl/cgi-bin/primer3-

plus/primer3plus.cgi, Last accessed November 16, 2015).

Primer sequences and their respective annealing temperatures

are listed in supplementary table S2, Supplementary Material

online. DNA extraction was performed by using the Dneasy

Plant Mini Kit (QIAGEN, Valencia, CA) on lyophilized fungal

cultures that were grown at room temperature for 10 days in

a 2% (w/v) malt extract liquid medium (AppliChem GmbH,

Darmstadt, Germany). Polymerase chain reaction (PCR) assays

were performed in a 25ml volume containing 5� PCR buffer,

1.5 mM of MgCl2, 0.2 mM of dNTPs mix, 0.5mM each of the

primers, 0.025 U of GoTaq polymerase (Promega, Madison,

WI), and 0.1 ng of genomic DNA. PCR reactions were con-

ducted as follows: an initial cycle with a 96 �C denaturation

step of 5 min, followed by 35 cycles, with each cycle consisting

of a 96 �C denaturation step of 30 s, an annealing step of 30 s

and a 72 �C extension step of 45 s, and one final cycle with a

72 �C extension step of 10 min. Amplicons were digested by



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ExoSAP-IT (Affymetrix, Santa Clara, CA) at 37 �C for 15 min

and then at 80 �C for 15 min. The PCR products were se-

quenced in both directions by the Functional Genomics

Laboratory of the University of Berkeley (CA). Sequences

were aligned using the algorithm ClustalW in MEGA v.6.0

(Tamura et al. 2013) with default parameters.

Identification of Highly Conserved and Highly DivergentGene Families in Genomic Regions Shared between theTwo Species

The snpEff analysis generated a tab-separated file in which

putative H. annosum SNPs/InDels were identified for each an-

notated gene model of H. irregulare. After gene length nor-

malization, genes harboring less than ten SNPs/InDels per

kilobase (nucleotide identity of more than 99%) putatively

associated with H. annosum were considered strongly con-

served, whereas genes with SNP density higher than 40

SNPs per kilobase (nucleotide identity of less than 96%)

were considered as highly divergent and species-specific. A

BLAST2GO analysis was used to characterize both conserved

and species-specific genes. The GOSSIP program in

BLAST2GO was used to perform Fisher’s exact tests with

FDR control in order to compare GO distributions of conserved

and species-specific genes with distributions predicted by all

H. irregulare gene models.

Genes influenced by speciation events (i.e., selection) were

identified calculating dN and dS substitution rates for each

gene affected by nonsynonymous SNPs/InDels. The dN/dS

ratio has been widely used to determine the mode of selec-

tion. Ratio of dN/dS >1 is interpreted as a sign of positive

selection, that is, natural selection promotes changes in the

protein sequence; whereas dN/dS <1 is generally accepted as

a sign of purifying selection, where some replacement substi-

tutions have been purified by natural selection, presumably

because of their deleterious effects (Hurst 2002). The panel

of detected putative H. annosum SNPs was annotated in ho-

mologous H. irregulare gene models by using snpEff. This

software listed the number of detected synonymous (Sd)

and nonsynonymous SNPs (Nd) for each gene, compared pair-

wise. The program KaKs_calculator (https://code.google.com/

p/kaks-calculator/downloads/list, Last accessed November 16,

2015) was used to calculate the number of expected synon-

ymous (S) and nonsynonymous (N) sites for each gene with

parameters set according to the Nei–Gojobori method.

The proportions of nonsynonymous and synonymous dif-

ferences between the two species for each gene compared

pairwise (pN and pS, respectively) were calculated with the

following formulas (Nei and Gojobori 1986):

pN ¼Nd

N;pS ¼

Sd

S:

The dN/dS ratio for each gene pair was then calculated with

the following formulas:

dN ¼ �3

4ln 1�

4pN

3

� �; dS ¼ �

3

4ln 1�

4ps

3

� �; dN=dS ¼

dN

dS:

The dN/dS ratios of genes related to saprobic growth, genes

related to fruiting body formation, and genes related to path-

ogenicity (Olson et al. 2012) were compared with the mean

dN/dS ratio of the whole gene data set through a permutation

t-test (9,999 permutation replicates).

Phylogenomic Analysis

Phylogenomic analysis was carried out with the software

REALPHY (reference sequence alignment-based phylogeny

builder) (Bertels et al. 2014) using raw reads of the six se-

quenced genotypes and sequence data from the H. irregu-

lare TC 32-1 genome. REALPHY inferred phylogenetic trees

from whole-genome sequence data based on all provided

sequences mapped to the reference genome through

bowtie2 (Langmead et al. 2009). Phylogenetic trees were

inferred on PhyML (phylogenetic estimation using maximum

likelihood) (Guindon et al. 2010), and a bootstrap consensus

tree was created (1,000 bootstrap replicates, initial tree

BioNJ, model of nucleotides substitution GTR [general time

reversible]). The phylogenetic analysis was carried out using

the alignment of sequenced reads of the six sequenced ge-

notypes on the coding sequences (CDSs) of the reference H.

irregulare TC 32-1.

SSR Analysis

An analysis of SSRs was performed on de novo assembly

drafts using the MISA mode of SciRoko software (Kofler

et al. 2007), with the minimum number of scored repeats

set at 14, 7, 5, 4, 4 and 4 for mono-, di-, tri-, tetra-, penta-

and hexanucleotides, respectively.

Results

Genome Sequencing, Mapping, and De Novo Assembly

The number of sequenced reads for each genotype was ap-

proximately 8 million. The percentages of PE reads that

aligned to the reference genome ranged from 87.59 to

92.22 for H. irregulare genotypes (9OA, 48NB, and 49SA)

and from 75.90 to 79.61 for H. annosum genotypes

(137OC, BM42NG, and 109SA). Sequence coverage ranged

between 17� and 22�. Only about 85% of H. irregulare and

70% of H. annosum PE reads were properly mapped. The

remaining aligned reads showed an abnormal insert size,

highlighting inter- and intraspecific variations in genome ar-

chitecture (table 2). Unmapped reads of H. annosum geno-

types were assembled in 1,104 contigs. AUGUSTUS predicted

249 putative CDSs. After the BLAST2GO analysis, 73 se-

quences were annotated as related to gag-pol polyproteins,

retroelements, retrotransposon nucleocapsid proteins and

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reverse transcriptases, whereas 176 showed no BLAST (Basic

Local Alignment Search Tool) hits.

De novo assembly of reads resulted in 5,262 contigs for

genotype 137OC, 4,686 for BM42NG, 4,994 for 109SA,

6,034 for 9OA, 6,992 for 48NB, and 6,119 for 49SA. N50

values ranged from 12.9 to 24 kb. A total of 14 scaffolds for

each genome were reconstructed. Sizes of final assemblies

ranged from 26.3 to 27.9 Mb. De novo assemblies were smal-

ler than those from the reference genome (33.6 Mb) (table 3).

Identification of Putative SVs

The number of SVs between H. irregulare and H. annosum

that were shared by all three H. annosum genotypes varied

between 1 and 49, depending on scaffold (table 4). The dis-

tribution of large deletions and insertions was not significantly

different among scaffolds (P value>0.05), whereas the distri-

bution of inversions and translocations varied significantly

among scaffolds (P value< 0.05). Scaffold_04, Scaffold_07,

and Scaffold_10 harbored the highest number of inversions

and translocations. Moreover, a single intrascaffold transloca-

tion was found in Scaffold_10. Putative SVs detected in H.

annosum and their position with respect to reference

genome are visualized in figures 1 and 2 and listed in supple-

mentary table S3, Supplementary Material online.

Comparative analyses among de novo assembly drafts by

progressiveMauve confirmed the presence of intraspecific var-

iability (fig. 3). Large shared genomic regions as well as in-

verted blocks among genotypes were detected. Scaffold_07,

Scaffold_04, Scaffold_11 and Scaffold_13 showed the largest

differences between H. irregulare and H. annosum, possibly

suggesting that these scaffolds might contain species-specific

genomic regions.

Table 2

Statistics of Reads Mapping of the Three Heterobasidion irregulare and the Three Heterobasidion annosum Genotypes to Reference Genome

Heterobasidion irregulare Genotypes Heterobasidion annosum Genotypes

9OA 48NB 49SA 137OC BM42NG 109SA

PE reads sequenced 8,036,722 8,025,191 8,028,750 8,018,594 8,018,514 8,020,180

Mapped reads 7,039,599 (87.59) 7,313,645 (91.13) 7,404,292 (92.22) 6,148,803 (76.68) 6,383,225 (79.61) 6,086,921 (75.90)

Properly mapped Reads 6,618,004 (82.35) 6,955,953 (86.68) 7,051,281 (87.83) 5,679,959 (70.83) 5,906,955 (73.67) 5,650,323 (70.45)

Singletons 63,510 (0.79) 57,368 (0.71) 62,502 (0.78) 206,180 (2.57) 207,745 (2.59) 188,937 (2.36)

Coverage (�) 20.52 21.78 21.61 16.97 17.66 16.86

NOTE.—Values in parentheses are given in percentage.

Table 4

Number of Putative Heterobasidion annosum SVs Divided in Intra- and

Interchromosomal for Each Scaffold

Intra Inter

Large

Insertions

(>2 kb)

Large

Deletions

(>2 kb)

Inversions Trans-

locations

Trans-

locations

Scaffold_01 2 2 3 0 1

Scaffold_02 1 3 5 0 3

Scaffold_03 4 2 5 0 1

Scaffold_04 3 5 15 0 49

Scaffold_05 2 2 10 0 5

Scaffold_06 0 0 0 0 4

Scaffold_07 2 3 24 0 7

Scaffold_08 2 4 9 0 10

Scaffold_09 1 1 1 0 1

Scaffold_10 4 4 23 1 31

Scaffold_11 2 2 12 0 3

Scaffold_12 3 3 9 0 19

Scaffold_13 0 0 5 0 15

Scaffold_14 1 2 5 0 16

NOTE.—Scaffold number is referred to the reference genome ofHeterobasidion irregulare.

Table 3

Statistics of De Novo Assemblies

Heterobasidion irregulare Genotypes Heterobasidion annosum Genotypes

9OA 48NB 49SA 137OC BM42NG 109SA

Contigs (n) 6,034 6,992 6,119 5,262 4,686 4,994

N50 24,007 12,945 14,781 22,892 24,566 22,448

Max contig length (bp) 139,331 194,148 129,618 145,724 220,315 175,157

Total length (bp) 26,374,808 26,374,274 26,844,330 27,696,343 27,988,318 27,530,324

Unassembled contigs (n) 1,694 1,984 1,551 1,578 1,385 1,492



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FIG. 1.—Visualization of putative H. annosum SVs and SNPs density for each scaffold. Each of the 14 scaffolds corresponding to chromosomes of the

reference H. irregulare TC32-1 is circled and defined. Starting from the outside, circles represent gene density in a window size of 10 kb (color coded from

yellow to dark red, with deeper red region representing high gene density), read depth of the representative H. irregulare genotype 49SA (pink histogram),

read depth of the representative H. annosum genotype 137OC (cyan histogram). SNP density of H. annosum estimated as density of consensus SNPs of three

H. annosum genotypes different from SNPs panel of H. irregulare genotypes (black line plot). Putative H. annosum SVs are represented as triangles and color

coded as follows: red for large deletions (>2 kb), green for large insertions (>2kb), and blue for inversions.

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Cumulatively, annotated genes inside inversions were 223,

whereas genes detected in translocations were 63. Among

these 63 genes, 14 were described as containing zinc-

finger-like domains and Gag domains related to retroviruses

and retrotransposons. Fisher’s exact test for enrichment anal-

yses on genes in H. annosum-inverted regions showed that

GO terms related to mitochondrial factors were overrepre-

sented (FDR-corrected P value<0.05) (supplementary table

S4, Supplementary Material online). In translocated regions,

GO terms GO:0008270 (zinc ion binding) and GO:0003676

(nucleic acid binding) were found to be overrepresented (for

details, see supplementary table S5, Supplementary Material

online).

Identification of Putative CNVs

Putative CNVs were more frequently identified at the begin-

ning of Scaffold_01, Scaffold_04, Scaffold_10, in Scaffold_13

(both telomeric regions), and in Scaffold_05 (about 100 kb

from one end). Additionally, CNVs were present but less

FIG. 2.—Visualization of putative H. annosum interchromosomal translocations and CNV along scaffolds. Heatmap representing gene density in a

window size of 100 kb is color coded from yellow to dark red, with deeper red representing high gene density. (A) Putative interchromosomal translocations

are represented as orange lines in the central part of the circle. Red lines are translocations supported by more than 30 reads. (B) CNVs were counted and

plotted in a sliding window size of 2kb and log2 ratios were calculated for all mapped hits. Only significant values (P value< 0.05) are visualized and peaks on

y axis represent a possible CNV event. Consistent CNVs (log2 > 5) are circled.



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frequent in Scaffold_07 and Scaffold_08 (fig. 2B). In genomic

regions affected by significant CNV events (P value<0.05,

log2 > 5), 36 genes were identified. Fisher’s exact test on

these 36 genes showed that only the term GO:0003676 (nu-

cleic acid binding) was significantly overrepresented compared

with all H. irregulare gene models (for details, see supplemen-

tary table S6, Supplementary Material online).

Identification of Putative SNPs and InDels

The number of consensus SNPs/InDels shared by all H. anno-

sum genotypes and absent in all H. irregulare genotypes was

estimated at 674,015 (about 20 SNPs/kb) (table 5). More than

50% of SNPs were distributed in intergenic regions, whereas

36% were in exons, and 14% in introns. In CDSs, the number

of SNPs/InDels, normalized for sequence length, resulted as

high as 21.05 (SD 9.23). In addition, 10,637 small insertions

and 7,903 small deletions were predicted. SNP/InDel annota-

tion showed that about 68% of SNPs/InDels within exons

were silent, whereas the remaining 32% caused changes in

coding due to frameshift mutations. A total of 146,809 SNPs

differentiated the three H. irregulare genotypes naturalized in

Italy from the North American H. irregulare reference genome

(about four SNPs per kilobase).

Alignment of partial sequences of ten loci in additional

Heterobasidion genotypes allowed for the validation of the

putative H. annosum SNPs/InDels detected in the six whole-

genome surveys. In these loci, 159 SNPs/InDels differentiating

the two species were detected. All putative H. annosum SNPs/

InDels detected by comparative sequence analysis of the six

genomes were confirmed in the genotypes for which individ-

ual loci were sequenced (see supplementary alignment S1,

Supplementary Material online).

In detail, 9 H. annosum SNPs were detected in locus

104812, 26 in locus 105463, 5 in locus 124417, 8 in locus

148906, 20 in locus 150620, 6 in locus 153627, 10 in locus

174687, 18 in locus 43914, 29 in locus 56987, and 19 in locus

63659. In addition, one deletion of 6 bp was confirmed in

FIG. 3.—Results of comparative analysis of de novo assembly drafts. The six genomes were compared using progressiveMauve (Darling et al. 2010) and

visualized using genoPlotR (Guy et al. 2010). Shared blocks are linked by dark red lines, whereas translocated blocks are linked by blue lines. Inverted blocks

are visualized as blocks below the colored bars representing the genomes.

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locus 105463, one deletion of 5 bp in locus 124417, and one

deletion of 3 bp in locus 56987. A small insertion of 2 bp was

also confirmed for locus 105463. Normalization for sequence

length of the number of putative H. annosum SNPs/InDels

detected in the ten loci analyzed resulted in an SNP density

of 22.20 SNPs/InDels per kilobase. In particular, the density of

polymorphism differentiating the two species was 31.35

SNPs/InDels for loci related to saprobic growth, 21.25 SNPs/

InDels per kilobase for loci associated with sporulation, and

20.43 SNPs/InDels per kilobase for loci associated with

pathogenicity.

Identification of Highly Conserved and Highly DivergentGene Families in Genomic Regions Shared between theTwo Species

The number of conserved genes showing more than 99% of

nucleotide identity between the two species was 690.

Conversely, 707 H. annosum genes were found to harbor

more than 40 putative SNPs/InDels per kilobase (nucleotide

identity of less than 96%) and may be regarded as species-

specific alleles. Main GO terms (GO terms assigned to more

than ten sequences) related to Molecular Function in con-

served genes and species-specific alleles are summarized in

supplementary figure S1, Supplementary Material online.

The comparison between GO terms assigned to both con-

served genes and species-specific alleles showed a significant

overrepresentation of terms GO:0003676 (oxidoreductase ac-

tivity) and GO:0020037 (heme binding) in species-specific al-

leles. On the other hand, GO terms related to ribosomal,

cellular metabolic processes, and signal transduction were sig-

nificantly overrepresented in the data set of conserved genes

when compared with species-specific alleles (supplementary

table S7, Supplementary Material online).

By analyzing SNPs in CDSs, 6,636 gene models were found

to contain putative nonsynonymous H. annosum SNPs. After

gene length normalization, an average of 10.25 nonsynon-

ymous SNPs per gene was found (SD 9.64). The average ratio

of the number of nonsynonymous substitutions per nonsyn-

onymous site to the number of synonymous substitutions per

synonymous site (dN/dS ratio) in H. annosum genome com-

pared with H. irregulare was 0.29 (SD 0.39) (fig. 4). Genes

involved in saprobic growth (i.e., genes significantly upregu-

lated during growth on wood; Olson et al. 2012) were 61 and

had a dN/dS ratio of 0.24 (SD 0.32), whereas genes associated

with fruiting body formation (i.e., genes significantly upregu-

lated in fruiting body compared with mycelium growth in

liquid medium; Olson et al. 2012) were 81 and had an average

dN/dS ratio of 0.21 (SD 0.23). Genes related to pathogenesis

(i.e., genes significantly upregulated in necrotic bark tissue;

Olson et al. 2012) were 42 and had an average dN/dS ratio

of 0.16 (SD 0.19). A permutation t-test comparing each cat-

egory to the ratio of whole genome determined that only the

dN/dS of genes related to pathogenesis was significantly

Table 5

Classification of Heterobasidion annosum Annotated Putative SNPs/

InDels

Putative Heterobasidion annosum SNPs/InDels

Number 674,015

SNPs/InDels distribution

Exons 217,606

Introns 97,306

Intergenic regions 359,103

SNP type

Transitions

A/G 148,866

C/T 117,640

G/A 117,697

T/C 149,031

Transversions

A/C 20,795

A/T 15,384

C/G 18,847

G/T 17,355

C/A 17,677

T/A 15,248

InDel type

Small insertions 10,637

Small deletions 7,903

Number of effects by functional class (%)

Missense 67,303 (31.175)

Nonsense 381 (0.176)

Silent 148,206 (68.649)

FIG. 4.—The dN/dS distribution among homolog pairs of H. irregulare

and H. annosum. The mean dN/dS value was 0.29 and is indicated by a red

line. Black line indicates the neutral expectation where dN = dS. In total,

153 sequences fall above the black line.



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different from the average dN/dS value (difference between

means = 0.16, t =�2.6, P = 0.009). Genes with a dN/dS ratio

>1 were 153, and were characterized using BLAST2GO

(supplementary table S8, Supplementary Material online).

Fisher’s exact test on these sequences showed a significant

(FDR-corrected P value< 0.05) overrepresentation of several

GO terms related to mitochondrial components, mitochon-

drial functions, transcriptional functions, and metal homeosta-

sis (supplementary table S9, Supplementary Material online).

Phylogenomic Analysis

Whole-genome phylogenetic analyses performed by using

REALPHY (Bertels et al. 2014) resulted in a consensus tree

clearly showing two distinct clades. Genotypes of H. annosum

clustered together in one clade, whereas H. irregulare geno-

types grouped separately and in the same clade as the refer-

ence genome (fig. 5).

SSR Analysis

Results of SSR analysis are summarized in table 6. The raw

number of SSRs in H. annosum ranged between 58.27 and

62.88 SSRs per megabase depending on genotype, whereas

that in H. irregulare ranged between 70.98 and 74.17 per

megabase, again depending on genotype. Although the

number of mononucleotide SSRs in H. irregulare genotypes

was almost twice as higher than that of H. annosum, differ-

ences were not significant (permutation t-test, P = 0.089).

Discussion

Heterobasidion irregulare and H. annosum Are ClearlyDistinct Species

Despite the high morphological similarity between H. irregu-

lare and H. annosum (Otrosina and Garbelotto 2010), evi-

dence based on isozyme and phylogenetic analyses limited

to a few loci (Otrosina et al. 1993; Linzer et al. 2008;

Dalman et al. 2010; Gonthier and Garbelotto 2011) has

shown that the two taxa have attained reciprocal monophyly

and are distinct based on the phylogenetic species concept

(Taylor et al. 2000). However, definitive evidence on their

status as distinct species was still lacking. Our phylogenetic

analysis on whole-genome sequences proved without any

doubt that H. irregulare is clearly distinct from H. annosum.

The Main Structure of the Genomes of the Two SpeciesHas Remained Similar

In spite of the long time since divergence and long allopatric

history, the two genomes appeared to be largely syntenic

and congruous. The macrosynteny between the two species

described in this study may be somewhat spurious due to

the fact that a reference genome of H. annosum is not avail-

able, and the six newly sequenced genomes representing

the two species necessarily had to be referenced to the

only annotated and publicly available H. irregulare

genome. Nonetheless, the alignment of assembly drafts

(fig. 3) showed high number of shared genomic blocks

among genomes. As mentioned above, we recognize that

this approach may not properly allow to exhaustively deter-

mine whether genomes of the two are truly congruent or

not, as it is biased by low coverage and quality of the pro-

duced contigs. However, taking into consideration the high

rate of hybridization between the two species (Garbelotto

and Gonthier 2013), these results can be regarded at least as

suggestive of significant levels of macrosynteny.

High genomic similarity between the two species is corrob-

orated by the fact that the entire genome of H. irregulare was

covered by 75% of H. annosum reads, and that nucleotide

interspecific homology reached 98% in several mapped ge-

nomic regions. Unmapped H. annosum reads were found to

harbor sequences related to retroelements, thus suggesting

that abundance of these elements may have contributed to

shape those genomic regions that were found to be most

divergent between the two species. In spite of the presence

of regions that were clearly different between the two species,

overall genome sizes, determined by comparing assembly

drafts, were similar (26.3–27.9 Mb), with H. annosum ge-

nomes slightly larger than H. irregulare genomes.

Although size of the three newly sequenced H. irregulare

genomes appeared to be different from that of the reference

genome, it should be noted that distinct sequencing

FIG. 5.—Phylogenetic relationships among sequenced genotypes and

H. irregulare reference genome as inferred by REALPHY through the align-

ment of reads on CDSs of reference genome. Only bootstrap values higher

than 50% are shown.

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approaches may generate artifacts. In this study, the above-

mentioned intraspecific difference in size should be regarded

as a result of variability between traditional Sangerian and

Illumina-based new generation sequencing methods. In ad-

dition, the difference in length between the new assemblies

and the reference genome could be affected by the presence

of repetitive sequences, that is, transposable elements (TEs),

viruses, and rDNA repeats. In fact, TEs in the genome of H.

irregulare were estimated to be as high as 16.2% of the

whole genome. This number was also supported by the

identification of TEs in the set of unmapped reads of H.

annosum. TEs may also have negatively affected the assem-

bly processes, as reported for the de novo assembly draft of

H. occidentale (Lind et al. 2012), further explaining some of

the differences reported here.

Inversions, Translocations, and CNVs Have Differentiatedthe Two Genomes

In our survey, putative H. annosum SVs were detected.

Genomic SVs, including deletions, insertions, CNVs, inversions

Table 6

Distribution of SSRs in the Six Analyzed Genomes

Genotype Motif Counts Average Length Counts/Mb

137OC

No. SSRs 2,003 Mononucleotide 50 21.26 1.45

Average length 20.92 Dinucleotide 175 17.58 5.09

Average SD 5.79 Trinucleotide 880 19.05 25.60

Counts/Mb (whole genome) 58.27 Tetranucleotide 474 20.16 13.79

Pentanucleotide 171 23.98 4.97

Hexanucleotide 253 29.02 7.36

BM42NG







109SA







9OA



Average SD 6.17 Trinucleotide 1,030 19.27 29.84




48NB







49SA



Average SD 5.62 Trinucleotide 1,029 19.00 29.69






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and translocations, are generally referred to as genomic rear-

rangements bigger than 1–2 kb (Alkan et al. 2011). The align-

ment of H. irregulare and H. annosum reads on the reference

genome allowed to identify putative SVs between the two

fungal species, removing the bias due to intraspecific variabil-

ity. The comparison of de novo assembly drafts was used to

confirm the presence of SVs. Based on our conservative com-

parative approach, SVs not shared by all isolates of one species

were discarded. We also noticed that some SVs, that is, inver-

sions and interchromosomal translocations, appeared not to

be equally distributed across scaffolds: for example, H. anno-

sum Scaffolds 04, 07, 11, and 13 were distinguishable from

matching H. irregulare scaffolds due to the presence of inver-

sions and translocations.

Several telomeric and subtelomeric regions of scaffolds of

the H. annosum genome were affected by CNV events. It has

been reported that fungal pathogens may show relevant

genome plasticity due to redundancy related to virulence

traits occurring in telomeric regions (Chuma et al. 2011;

Raffaele and Kamoun 2012; Stukenbrock 2013) and adapta-

tion to new environments (Denayrolles et al. 1997; Chow

et al. 2012). SSR analyses also showed that mononucleotide

repeats were more abundant in H. irregulare than in H. anno-

sum genomes, although not significantly. As SSR analysis was

performed on de novo assembly drafts, it should not have

been biased by the use of H. irregulare as a reference. Given

that H. annosum is presumed to be ancestral to H. irregulare

(Otrosina et al. 1993; Linzer et al. 2008; Dalman et al. 2010),

mononucleotide repeats might be correlated to divergent

evolution.

Species-Specific Alleles Were Related to Heme BindingProteins and to Oxidoreductases

Alignment of reads of the six genomes in relation to the ref-

erence genome allowed to identify putative H. annosum SNPs/

InDels absent in H. irregulare genotypes. At the intraspecific

level, SNPs density detected within H. irregulare genotypes

(about four SNPs per kilobase) was consistent with those re-

ported for other basidiomycetes species, such as Lentinula

edodes (4.6 SNPs per kilobase; Au et al. 2013) and

Melamspora larici-populina (about six SNPs per kilobase;

Persoons et al. 2014). On the other hand, interspecific se-

quence polymorphisms were estimated as high as about 20

SNPs per kilobase. A set of 159 SNPs/InDels were verified and

confirmed by the sequencing of ten additional loci in ten iso-

lates, equally representing the two Heterobasidion species.

Conserved genomic regions shared between the two spe-

cies were assumed to harbor genes related to primary metab-

olism and to survival, whereas genes in less conserved regions

might be related to other pathways (e.g., secondary metabo-

lism). When H. annosum genotypes were compared with H.

irregulare genotypes, 690 genes were regarded as highly con-

served and had more than 99% of nucleotide identity. On the

contrary, 707 alleles harbored high SNPs density resulting in

less than 96% of nucleotide identity between the two fungi.

The most overrepresented terms among species-specific al-

leles were related to oxidation-reduction processes (66 of

707 genes with this term) and heme binding proteins (18 of

707 genes). It has been reported that the H. irregulare

genome contains a versatile set of oxidoreductases putatively

involved in lignin oxidation and conversion, including glyoxal

oxidases, quinone-oxidoreductases, and aryl-alcohol oxidases

(Olson et al. 2012). In addition, wood decay fungi as

Heterobasidion are known to produce large amounts of

heme-containing proteins, such as manganese and lignin per-

oxidases (MacDonald et al. 2012). Lignin peroxidases are

among the main enzymes involved in lignin degradation. In

a transcriptomics study using H. annosum as a model system,

five manganese peroxidases were found to be specifically in-

duced only during saprobic growth (Raffaello et al. 2014). One

possible interpretation of the abundance of SNPs/InDels in

genes encoding these classes of enzymes could be that they

have accumulated mutations during the different adaptive

evolution of the two fungal species.

Genes Showing High Values of dN/dS Ratio Were MainlyRelated to Transcriptional Activity and MitochondrialFactors

Nonsynonymous mutations are generally predicted to contrib-

ute to phenotypic evolution more than synonymous muta-

tions. In fact, nonsynonymous mutations directly alter the

amino acid sequence and are likely to affect protein stability

and activity. In our comparisons, only 32% of SNPs/InDels

putatively associated with H. annosum coding regions lead

to changes in proteins. In particular, approximately 6,600

genes were found to harbor nonsynonymous SNPs between

the two species. To evaluate evolutionary pressure acting on

genes affected by SNPs/InDels, we estimated the dN/dS ratio

between orthologous sequences. Results showed that a ma-

jority of sequence pairs (about 95%) had a dN/dS ratio <1,

suggesting that these genes covering a wide array of functions

evolved under purifying selection without altering the

encoded amino acid sequence during the speciation. Loci af-

fected by dN/dS ratios >1 were instead found to be mostly

related to transcriptional activity. Transcriptional regulation

may trigger several biological processes in a cell or in an or-

ganism, both in primary metabolic and physiological balance,

and in responses to the environment (Riechmann et al. 2000).

In fungi, the comparison of the transcriptional regulatory net-

works of several ascomycetes suggested that regulatory ele-

ments of metabolic pathways have dramatically changed

between species and seem extremely plastic (Carroll 2000;

Tuch et al. 2008; Lavoie et al. 2009). It could be hypothesized

that both large fractions of SNPs on noncoding regions which

might represent cis-regulatory elements, that is, enhancers,

promoters, 50-untranslated regions (UTRs), 30UTRs, introns,

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as well as nonsynonymous mutations in transcriptional factors,

possibly leading to a rewiring of gene expression regulation,

may have been involved in the divergence between H. irregu-

lare and H. annosum. The extensive proliferation of nonsyn-

onymous SNPs in genes related to transcriptional activities may

reflect the diversification of the regulatory pathways of these

two pathogens. According to this scenario, differences in tran-

scription regulation between these two sibling species may be

responsible for rapid adaptive evolution. Interestingly, a

genome-wide association study performed by Dalman et al.

(2013) showed that one of the 14 mutations significantly as-

sociated with virulence traits in H. annosum is a synonymous

SNP into an SWI5 transcription factor encoding gene, suggest-

ing that this phenotypic trait could also be influenced by

changes in transcriptional network. The homologous of

SWI5 in the yeast Candida albicans was shown to affect viru-

lence and morphogenesis (Kelly et al. 2004).

Fisher’s exact test for enrichment of GO terms on genes

identified as affected by positive selection showed also an

enrichment of functional categories related to mitochondrial

functions. Most of the mitochondrial functions are encoded

by nuclear genes. Mitochondrial bioenergetics has been re-

cently proposed as a potential major force in adaptive evolu-

tion and even speciation processes through coevolution of

mitochondrion and nuclear-encoded mitochondrial genes

(Gershoni et al. 2009). In several fungal pathogens including

Heterobasidion, it has been shown that mitochondria affect

virulence (Olson and Stenlid 2001; Garbelotto et al. 2007;

Shingu-Vazquez and Traven 2011).

SVs Harbored Genes Related to Mitochondrial Functions,TEs, and Nucleic Acid Binding

The presence of SVs disrupting microsynteny between the

genomes of the two species might have lead to the creation

of small genomic islands harboring ecologically important

genes with higher rates of evolution, as it has been docu-

mented for genes involved in adaptation to temperature on

Neurospora species (Ellison et al. 2011). The gene models de-

tected in inversions, interchromosomal translocations, and re-

gions affected by CNV events were characterized in silico by

using BLAST2GO. In inverted regions, the main overrepre-

sented GO terms were related to processes involved in protein

targeting to mitochondrion and mitochondrial inner mem-

brane peptidase complex, indicating that these SVs contain

genes related to protein involved in mitochondrial factors.

Among genes in regions affected by interchromosomal trans-

locations events, 14 of 63 were annotated as encoding for

Gag or capsid-related retrotransposon-related proteins. TEs

promote chromosomal rearrangements more efficiently than

other cellular processes, and TEs have been proposed as dri-

vers of plant pathogen genome evolution due to the fact that

they may mediate chromosomal rearrangements by ectopic

recombination (Schmidt and Panstruga 2011). The

documented proliferation of mobile elements in the genome

of H. irregulare (Olson et al. 2012) and the presence of se-

quences related to retrotransposons in putative interchromo-

somal translocations indicated that the activity of TEs may

have played a role in the differentiation of the H. irregulare

genome from that of H. annosum. In addition, the overrepre-

sented GO terms in interchromosomal translocations indicate

that these SVs also contain genes related to mitochondrial

functions.

Overrepresentation of genes related to nucleic acid binding

proteins in regions affected by CNV events in H. annosum

suggests that they might be involved in regulation of gene

expression, acting as enhancers thanks to their redundancy.

It could be inferred that H. irregulare may have lost this type of

redundancy present in a common ancestor, or alternatively

that H. annosum may have evolved subtelomeric and telo-

meric redundancy as a result of selective pressure events in

its Eurasian ecological niche, in which it coexists with other

competitive Heterobasidion species (Garbelotto and Gonthier

2013).

Genes Related to Pathogenicity Are More Conservedthan Genes Involved in Saprobic Processes and FruitingBody Formation

Olson et al. (2012) have shown a clear trade-off between H.

irregulare gene families expressed during pathogenesis, sapro-

bic wood decay, and fruiting. Thus, the higher saprobic

growth and fruiting potential, demonstrated for H. irregulare

compared with H. annosum (Garbelotto et al. 2010; Giordano

et al. 2014), should be confirmed at the genomic level by the

presence of substantial interspecific differences in genes in-

volved in these two last functions. The presence of nonsynon-

ymous SNPs, of SVs, and the dN/dS ratio in regions harboring

genes related to pathogenesis, saprobic ability, and fruiting

are in agreement with the documented phenotypic observa-

tions. In fact, the significant difference between dN/dS values

of pathogenesis genes versus the entire gene data set sug-

gests that these genes have undergone purifying selection and

are conserved in both species. In contrast, genes related to

saprobic ability and fruiting body formation appeared to have

evolved at rates comparable to those of the entire gene data

set. A more “relaxed” purifying selection pressure could be

inferred for these genes that appear to have tolerated higher

densities of nonsynonymous mutations compared with path-

ogenesis-related genes.

Conclusions

In conclusion, our comparative analyses provide insights on

genomic differences between two closely related plant path-

ogens. SVs including inversions, translocations, and CNVs

have played a prominent role in the creation of genomic is-

lands leading to diversification of the two species. In addition,

adaptive evolution might have remodeled their transcriptional



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and post-transcriptional machinery, their mitochondrial-re-

lated pathways, and their pattern of mobile elements.

Genes encoding heme binding proteins and oxidoreductases

exclusively found in regions showing high level of sequence

variation might also have been influenced by adaptive pro-

cesses. Finally, genes involved in sporulation and especially in

saprobic growth appeared to be more variable between the

two species, compared with genes involved in pathogenicity.

This result provides genomic evidence that differences in fit-

ness between the two species are likely to involve saprobic

growth and sporulation, two functions positively affecting

transmission but not directly involved in pathogenesis.

Further approaches, including postgenomic studies and

phenotypic experiments, will allow to understand how specific

molecular mechanisms may have evolved during the allopatric

speciation of the two sister species. Transcriptomic

approaches (i.e., RNA-sequencing) will be pivotal to verify

whether transcriptional responses are species specific, thus

confirming that allopatric speciation may have influenced

the transcriptional and post-transcriptional activities of con-

served genes between the two species.

Supplementary Material

Supplementary alignment S1, figure S1, and tables S1–S9 are

available at Genome Biology and Evolution online (http://

www.gbe.oxfordjournals.org/).

Acknowledgments

The authors are grateful to Guglielmo Gianni Lione for help in

statistical analyses and R scripting and to the anonymous re-

viewers for their helpful suggestions. This work was supported

by the Italian Ministry of Education, University and Research,

within the FIRB program (grant number RBFR128ONN).

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